MOTION OF RNA-POLYMERASE ALONG DNA - A STOCHASTIC-MODEL

RNA polymerase is a key transcription enzyme that moves along a DNA do uble helix to polymerize an RNA transcript. Recent progress in microme chanical experiments permits quantitative studies of forces and motion generated by the enzyme. We present in this paper a chemical kinetics description of RNA polymerase motion. The model is based on a classic al chemical kinetics description of polymerization reactions driven by a free energy gain that depends on forces applied externally at the c atalytic site. The RNA polymerase controlled activation barrier of the reaction is assumed to be strongly dependent on inhibitory internal s trains of the RNA polymerase molecule. The sequence sensitivity of RNA polymerase is described by a linear coupling between the height of th e activation barrier and the local DNA sequence. Our model can simulat e optical trap experiments and allows us to study the dynamics of chem ically halted complexes that are important for footprinting studies. W e find that the effective stall force is a sequence-dependent, statist ical quantity, whose distribution depends on the observation time. The results are consistent with the experimental observations to date.